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PDBsum entry 2or1
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Gene regulation/DNA
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PDB id
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2or1
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Contents |
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* Residue conservation analysis
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DOI no:
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Science
242:899-907
(1988)
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PubMed id:
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Recognition of a DNA operator by the repressor of phage 434: a view at high resolution.
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A.K.Aggarwal,
D.W.Rodgers,
M.Drottar,
M.Ptashne,
S.C.Harrison.
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ABSTRACT
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The repressors of temperate bacteriophages such as 434 and lambda control
transcription by binding to a set of DNA operator sites. The different affinity
of repressor for each of these sites ensures efficient regulation.
High-resolution x-ray crystallography was used to study the DNA-binding domain
of phage 434 repressor in complex with a synthetic DNA operator. The structure
shows recognition of the operator by direct interactions with base pairs in the
major groove, combined with the sequence-dependent ability of DNA to adopt the
required conformation on binding repressor. In particular, a network of
three-centered bifurcated hydrogen bonds among base pairs in the operator helps
explain why 434 repressor prefers certain sites over others. These bonds, which
stabilize the conformation of the bound DNA, can form only with certain
sequences.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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W.A.Hendrickson
(2013).
Evolution of diffraction methods for solving crystal structures.
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Acta Crystallogr A,
69,
51-59.
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E.S.Vanamee,
H.Viadiu,
S.H.Chan,
A.Ummat,
A.M.Hartline,
S.Y.Xu,
and
A.K.Aggarwal
(2011).
Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
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Nucleic Acids Res,
39,
712-719.
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PDB code:
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D.Wang,
N.B.Ulyanov,
and
V.B.Zhurkin
(2010).
Sequence-dependent Kink-and-Slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove.
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J Biomol Struct Dyn,
27,
843-859.
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F.van den Ent,
C.M.Johnson,
L.Persons,
P.de Boer,
and
J.Löwe
(2010).
Bacterial actin MreB assembles in complex with cell shape protein RodZ.
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EMBO J,
29,
1081-1090.
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PDB code:
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R.Rohs,
X.Jin,
S.M.West,
R.Joshi,
B.Honig,
and
R.S.Mann
(2010).
Origins of specificity in protein-DNA recognition.
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Annu Rev Biochem,
79,
233-269.
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T.Massad,
K.Skaar,
H.Nilsson,
P.Damberg,
P.Henriksson-Peltola,
E.Haggård-Ljungquist,
M.Högbom,
and
P.Stenmark
(2010).
Crystal structure of the P2 C-repressor: a binder of non-palindromic direct DNA repeats.
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Nucleic Acids Res,
38,
7778-7790.
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PDB code:
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I.Mruk,
and
R.M.Blumenthal
(2009).
Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system.
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Nucleic Acids Res,
37,
983-998.
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R.Rohs,
S.M.West,
A.Sosinsky,
P.Liu,
R.S.Mann,
and
B.Honig
(2009).
The role of DNA shape in protein-DNA recognition.
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Nature,
461,
1248-1253.
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M.S.Dubrava,
W.M.Ingram,
S.A.Roberts,
A.Weichsel,
W.R.Montfort,
and
M.H.Cordes
(2008).
N15 Cro and lambda Cro: orthologous DNA-binding domains with completely different but equally effective homodimer interfaces.
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Protein Sci,
17,
803-812.
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PDB code:
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Y.Shao,
L.S.Feldman-Cohen,
and
R.Osuna
(2008).
Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site.
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J Mol Biol,
380,
327-339.
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E.R.Schreiter,
and
C.L.Drennan
(2007).
Ribbon-helix-helix transcription factors: variations on a theme.
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Nat Rev Microbiol,
5,
710-720.
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K.Yamasaki,
T.Akiba,
T.Yamasaki,
and
K.Harata
(2007).
Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1.
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Nucleic Acids Res,
35,
5073-5084.
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PDB codes:
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R.Joshi,
J.M.Passner,
R.Rohs,
R.Jain,
A.Sosinsky,
M.A.Crickmore,
V.Jacob,
A.K.Aggarwal,
B.Honig,
and
R.S.Mann
(2007).
Functional specificity of a Hox protein mediated by the recognition of minor groove structure.
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Cell,
131,
530-543.
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PDB codes:
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S.C.Harrison
(2007).
Three-dimensional intricacies in protein-DNA recognition and transcriptional control.
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Nat Struct Mol Biol,
14,
1118-1119.
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L.S.Feldman-Cohen,
Y.Shao,
D.Meinhold,
C.Miller,
W.Colón,
and
R.Osuna
(2006).
Common and variable contributions of Fis residues to high-affinity binding at different DNA sequences.
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J Bacteriol,
188,
2081-2095.
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N.B.Becker,
L.Wolff,
and
R.Everaers
(2006).
Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.
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Nucleic Acids Res,
34,
5638-5649.
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S.J.Williamson,
and
J.H.Paul
(2006).
Environmental factors that influence the transition from lysogenic to lytic existence in the phiHSIC/Listonella pelagia marine phage-host system.
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Microb Ecol,
52,
217-225.
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W.A.Weihofen,
A.Cicek,
F.Pratto,
J.C.Alonso,
and
W.Saenger
(2006).
Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription.
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Nucleic Acids Res,
34,
1450-1458.
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PDB codes:
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E.S.Groban,
M.B.Johnson,
P.Banky,
P.G.Burnett,
G.L.Calderon,
E.C.Dwyer,
S.N.Fuller,
B.Gebre,
L.M.King,
I.N.Sheren,
L.D.Von Mutius,
T.M.O'Gara,
and
C.M.Lovett
(2005).
Binding of the Bacillus subtilis LexA protein to the SOS operator.
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Nucleic Acids Res,
33,
6287-6295.
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E.S.Vanamee,
H.Viadiu,
R.Kucera,
L.Dorner,
S.Picone,
I.Schildkraut,
and
A.K.Aggarwal
(2005).
A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
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EMBO J,
24,
4198-4208.
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PDB codes:
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M.R.Sawaya,
Z.Zhu,
F.Mersha,
S.H.Chan,
R.Dabur,
S.Y.Xu,
and
G.K.Balendiran
(2005).
Crystal structure of the restriction-modification system control element C.Bcll and mapping of its binding site.
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Structure,
13,
1837-1847.
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PDB code:
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C.Guarnaccia,
B.Raman,
S.Zahariev,
A.Simoncsits,
and
S.Pongor
(2004).
DNA-mediated assembly of weakly interacting DNA-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast GCN4 DNA-binding domains.
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Nucleic Acids Res,
32,
4992-5002.
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D.R.Pawlowski,
and
G.B.Koudelka
(2004).
The preferred substrate for RecA-mediated cleavage of bacteriophage 434 repressor is the DNA-bound dimer.
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J Bacteriol,
186,
1-7.
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S.Rumpel,
A.Razeto,
C.M.Pillar,
V.Vijayan,
A.Taylor,
K.Giller,
M.S.Gilmore,
S.Becker,
and
M.Zweckstetter
(2004).
Structure and DNA-binding properties of the cytolysin regulator CylR2 from Enterococcus faecalis.
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EMBO J,
23,
3632-3642.
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PDB code:
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B.Hartmann,
M.R.Sullivan,
and
L.F.Harris
(2003).
Operator recognition by the phage 434 cI repressor: MD simulations of free and bound 50-bp DNA reveal important differences between the OR1 and OR2 sites.
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Biopolymers,
68,
250-264.
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D.B.Hoggan,
J.A.Chao,
G.S.Prasad,
C.D.Stout,
and
J.R.Williamson
(2003).
Combinatorial crystallization of an RNA-protein complex.
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Acta Crystallogr D Biol Crystallogr,
59,
466-473.
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S.C.Sinha,
J.Krahn,
B.S.Shin,
D.R.Tomchick,
H.Zalkin,
and
J.L.Smith
(2003).
The purine repressor of Bacillus subtilis: a novel combination of domains adapted for transcription regulation.
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J Bacteriol,
185,
4087-4098.
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PDB codes:
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A.Vannini,
C.Volpari,
C.Gargioli,
E.Muraglia,
R.Cortese,
R.De Francesco,
P.Neddermann,
and
S.D.Marco
(2002).
The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA.
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EMBO J,
21,
4393-4401.
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PDB code:
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C.R.Escalante,
L.Shen,
D.Thanos,
and
A.K.Aggarwal
(2002).
Structure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter.
|
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Structure,
10,
383-391.
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PDB code:
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K.Steinmetzer,
J.Behlke,
S.Brantl,
and
M.Lorenz
(2002).
CopR binds and bends its target DNA: a footprinting and fluorescence resonance energy transfer study.
|
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Nucleic Acids Res,
30,
2052-2060.
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P.P.Papp,
T.Nagy,
S.Ferenczi,
P.Elõ,
Z.Csiszovszki,
Z.Buzás,
A.Patthy,
and
L.Orosz
(2002).
Binding sites of different geometries for the 16-3 phage repressor.
|
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Proc Natl Acad Sci U S A,
99,
8790-8795.
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Z.Morávek,
S.Neidle,
and
B.Schneider
(2002).
Protein and drug interactions in the minor groove of DNA.
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Nucleic Acids Res,
30,
1182-1191.
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D.C.Kombo,
K.J.McConnell,
M.A.Young,
and
D.L.Beveridge
(2001).
Molecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator.
|
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Biopolymers,
59,
205-225.
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M.L.Coté,
and
M.M.Georgiadis
(2001).
Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase.
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Acta Crystallogr D Biol Crystallogr,
57,
1238-1250.
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PDB code:
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T.Liang,
K.Tan,
K.Chong,
Z.Zhu,
S.Pongor,
and
A.Simoncsits
(2001).
Selection and design of high affinity DNA ligands for mutant single-chain derivatives of the bacteriophage 434 repressor.
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Sci China C Life Sci,
44,
274-286.
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D.C.Kombo,
M.A.Young,
and
D.L.Beveridge
(2000).
One nanosecond molecular dynamics simulation of the N-terminal domain of the lambda repressor protein.
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Biopolymers,
53,
596-605.
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J.Xu,
and
G.B.Koudelka
(2000).
DNA sequence requirements for the activation of 434 P(RM) transcription by 434 repressor.
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DNA Cell Biol,
19,
621-630.
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G.Caderas,
S.Klauser,
N.Liu,
A.Bienz,
and
B.Gutte
(1999).
Inhibition of HIV-1 enhancer-controlled transcription by artificial enhancer-binding peptides derived from bacteriophage 434 repressor.
|
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Eur J Biochem,
266,
599-607.
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J.Nowakowski,
P.J.Shim,
G.F.Joyce,
and
C.D.Stout
(1999).
Crystallization of the 10-23 DNA enzyme using a combinatorial screen of paired oligonucleotides.
|
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Acta Crystallogr D Biol Crystallogr,
55,
1885-1892.
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J.Ruiz-Sanz,
A.Simoncsits,
I.Törö,
S.Pongor,
P.L.Mateo,
and
V.V.Filimonov
(1999).
A thermodynamic study of the 434-repressor N-terminal domain and of its covalently linked dimers.
|
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Eur J Biochem,
263,
246-253.
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J.S.Hwang,
J.Yang,
and
A.J.Pittard
(1999).
Specific contacts between residues in the DNA-binding domain of the TyrR protein and bases in the operator of the tyrP gene of Escherichia coli.
|
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J Bacteriol,
181,
2338-2345.
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N.Zheng,
E.Fraenkel,
C.O.Pabo,
and
N.P.Pavletich
(1999).
Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP.
|
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Genes Dev,
13,
666-674.
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PDB code:
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O.Littlefield,
Y.Korkhin,
and
P.B.Sigler
(1999).
The structural basis for the oriented assembly of a TBP/TFB/promoter complex.
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Proc Natl Acad Sci U S A,
96,
13668-13673.
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PDB code:
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W.S.Tzou,
and
M.J.Hwang
(1999).
Modeling helix-turn-helix protein-induced DNA bending with knowledge-based distance restraints.
|
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Biophys J,
77,
1191-1205.
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F.X.Gomis-Rüth,
M.Solá,
P.Acebo,
A.Párraga,
A.Guasch,
R.Eritja,
A.González,
M.Espinosa,
G.del Solar,
and
M.Coll
(1998).
The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator.
|
| |
EMBO J,
17,
7404-7415.
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PDB codes:
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G.B.Koudelka
(1998).
Recognition of DNA structure by 434 repressor.
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Nucleic Acids Res,
26,
669-675.
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J.Woda,
B.Schneider,
K.Patel,
K.Mistry,
and
H.M.Berman
(1998).
An analysis of the relationship between hydration and protein-DNA interactions.
|
| |
Biophys J,
75,
2170-2177.
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N.Liu,
C.Deillon,
S.Klauser,
B.Gutte,
and
R.M.Thomas
(1998).
Synthesis, physicochemical characterization, and crystallization of a putative retro-coiled coil.
|
| |
Protein Sci,
7,
1214-1220.
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R.E.Dickerson
(1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.
|
| |
Nucleic Acids Res,
26,
1906-1926.
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Y.Mandel-Gutfreund,
and
H.Margalit
(1998).
Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites.
|
| |
Nucleic Acids Res,
26,
2306-2312.
|
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A.Nauta,
B.van den Burg,
H.Karsens,
G.Venema,
and
J.Kok
(1997).
Design of thermolabile bacteriophage repressor mutants by comparative molecular modeling.
|
| |
Nat Biotechnol,
15,
980-983.
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D.N.Paolella,
Y.Liu,
M.A.Fabian,
and
A.Schepartz
(1997).
Electrostatic mechanism for DNA bending by bZIP proteins.
|
| |
Biochemistry,
36,
10033-10038.
|
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J.Chen,
S.Pongor,
and
A.Simoncsits
(1997).
Recognition of DNA by single-chain derivatives of the phage 434 repressor: high affinity binding depends on both the contacted and non-contacted base pairs.
|
| |
Nucleic Acids Res,
25,
2047-2054.
|
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J.W.Schwabe
(1997).
The role of water in protein-DNA interactions.
|
| |
Curr Opin Struct Biol,
7,
126-134.
|
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L.Jen-Jacobson
(1997).
Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state.
|
| |
Biopolymers,
44,
153-180.
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L.Tucker-Kellogg,
M.A.Rould,
K.A.Chambers,
S.E.Ades,
R.T.Sauer,
and
C.O.Pabo
(1997).
Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity.
|
| |
Structure,
5,
1047-1054.
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PDB code:
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M.A.Kercher,
P.Lu,
and
M.Lewis
(1997).
Lac repressor-operator complex.
|
| |
Curr Opin Struct Biol,
7,
76-85.
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N.Pastor,
L.Pardo,
and
H.Weinstein
(1997).
Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein.
|
| |
Biophys J,
73,
640-652.
|
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R.E.Dickerson,
and
T.K.Chiu
(1997).
Helix bending as a factor in protein/DNA recognition.
|
| |
Biopolymers,
44,
361-403.
|
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R.M.Xu,
C.Koch,
Y.Liu,
J.R.Horton,
D.Knapp,
K.Nasmyth,
and
X.Cheng
(1997).
Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis.
|
| |
Structure,
5,
349-358.
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PDB code:
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D.A.Erlanson,
M.Chytil,
and
G.L.Verdine
(1996).
The leucine zipper domain controls the orientation of AP-1 in the NFAT.AP-1.DNA complex.
|
| |
Chem Biol,
3,
981-991.
|
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D.Carotti,
S.Funiciello,
P.Lavia,
P.Caiafa,
and
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EMBO J,
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Cell,
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PDB code:
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D.G.Brown,
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EMBO J,
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PDB code:
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D.T.Simmons,
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(1990).
Identification of simian virus 40 T-antigen residues important for specific and nonspecific binding to DNA and for helicase activity.
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J Virol,
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Nucleic Acids Res,
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PDB code:
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H.C.Pace,
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lac repressor: crystallization of intact tetramer and its complexes with inducer and operator DNA.
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Proc Natl Acad Sci U S A,
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Proc Natl Acad Sci U S A,
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PDB codes:
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J.Heitman,
and
P.Model
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Substrate recognition by the EcoRI endonuclease.
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Proteins,
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Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures.
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Proteins,
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L.D.Williams,
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Nucleic Acids Res,
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PDB code:
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M.Affolter,
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M.Müller,
W.Leupin,
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DNA binding properties of the purified Antennapedia homeodomain.
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Proc Natl Acad Sci U S A,
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Molecular recognition in the minor groove of the DNA helix. Studies on the synthesis of oligonucleotides and polynucleotides containing 3-deaza-2'-deoxyadenosine. Interaction of the oligonucleotides with the restriction endonuclease EcoRV.
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Nucleic Acids Res,
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Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex.
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Proc Natl Acad Sci U S A,
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PDB code:
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R.M.Lamerichs,
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Assignment of the 1H-NMR spectrum of a lac repressor headpiece-operator complex in H2O and identification of NOEs. Consequences for protein-DNA interaction.
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Saturation mutagenesis of the DNA site bound by the small carboxy-terminal domain of gamma delta resolvase.
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EMBO J,
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Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically.
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Proc Natl Acad Sci U S A,
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EMBO J,
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DNA binding specificity of steroid receptors.
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A single amino acid can determine the DNA binding specificity of homeodomain proteins.
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Cell,
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An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution.
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Flanking DNA-sequences contribute to the specific binding of cI-repressor and OR1.
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Determinants of EcoRI endonuclease sequence discrimination.
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Proc Natl Acad Sci U S A,
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R.G.Brennan,
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Structural basis of DNA-protein recognition.
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Trends Biochem Sci,
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The amino-terminal domain of LexA repressor is alpha-helical but differs from canonical helix-turn-helix proteins: a two-dimensional 1H NMR study.
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| |
Proc Natl Acad Sci U S A,
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S.D.Hanes,
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DNA specificity of the bicoid activator protein is determined by homeodomain recognition helix residue 9.
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| |
Cell,
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Y.Q.Qian,
M.Billeter,
G.Otting,
M.Müller,
W.J.Gehring,
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(1989).
The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: comparison with prokaryotic repressors.
|
| |
Cell,
59,
573-580.
|
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|
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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|
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